SMTL ID : 4j7m.1

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x U- U37- U37- U- U: RNA (5'-R(P*UP*(U37)P*(U37)P*UP*U)-3')(Non-covalent)

U-U37-U37-U-U.1: 20 residues within 4Å: Chain A: R.89, R.126, G.127, E.141, L.175, L.178, M.179, G.182, Y.183, E.186, E.228, E.247, L.248, K.249, T.250, K.252, K.267, Q.274, R.288 Ligands: CA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.250, A:R.288 Water bridges: A:T.250

2 x UBD: URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE)(Non-covalent)

UBD.2: 6 residues within 4Å: Chain A: R.24, T.25, Q.26, G.352, G.353, P.354 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.25, A:T.25, A:Q.26, A:Q.26, A:G.352 Water bridges: A:T.25 UBD.3: 7 residues within 4Å: Chain A: L.105, E.106, H.107, R.108, N.109, Q.110, T.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.109, A:Q.110 Water bridges: A:T.375 Salt bridges: A:R.108

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.230, E.247, L.248 Ligands: U-U37-U37-U-U.1, U-U37-U37-U-U.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.230, A:E.247, A:L.248, H2O.11, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiao, X. et al., A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. Mol.Cell (2013)

Release Date

2013-03-27

Peptides

Protein Dom3Z: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein Dom3Z

Related Entries With Identical Sequence